Hitman: Codename Shinji
by Baronvonblack
Summary: I never knew who I once was, nor do I care. Neither do I have a future. I live in the moment of every kill, of every life that I take. They said my name was once Shinji, now I am simply a number - 49.
1. Capture

"_Wake up."_

Shinji's bloodshot eyes opened.

He found himself attached to a bed by strong leather straps. In vain, he desperately tried to move, but to no avail. "W-Where am I? Who are you?!"

"_Who am I?" _the voice gave off a maniacal laugh. _"I am your guardian angel. Because of me, you were not killed by those cleaners that were sent to…straighten out a few things."_

Slowly, Shinji's memories began to return to him. "I was… walking down a street by a cafe when…"

-------

Shinji walked down a lonely street in Tokyo-3, more depressed than usual.

Everything was so messy – his father had been killed last night by a sniper. When the Sub-Commander took control over NERV, he told them all everything.

NERV's purpose. SEELE. Third Impact.

Frankly, all this disgusted Shinji.

He felt anger at being manipulated, fighting for a cause he didn't really believe in but thought was necessary, when in fact he was being deceived into carrying out the steps to mankind's destruction.

The pilot was sick of everything…he just wanted to die.

_Kaworu… _he looked down at his hands, remembering how he crushed the only friend he trusted. _Kaworu, why didn't you tell me this? Why didn't anyone tell me what was going on?_

Walking past a small café, he sat down at one of the wooden tables, his mind being heavily overweighed by everything that was processed this day.

"Call an ambulance!"

"It's too late, he's already dead!"  
Shinji looked around to see a strange sight.

Inside the café, several people surrounded the dead corpse of a man in a silk suit, some seemed to be security guards, others just people who wanted to help.

"Who was that bastard that shot him?"

"Where the hell are the cops?!"  
Suddenly, a large black van pulled up beside the café and men, dressed all in black army fatigues and wielding rifles with what appeared to be thick silencers on them poured out.

"Finally, the cops have arrived…HEY! WHAT ON EARTH ARE YOU…GAHHH!"

The man's shrieking was silenced by several muffled coughs from the men's rifles as they charged in, shooting anything that moved.

Shinji watched all this, wide-eyed and shocked.

One of the men turned towards him, locking eyes, cold calculating eyes.

Everything seemed to happen in slow motion for Shinji as he looked down to see the rifle aiming at him, the man's finger curling around the trigger.

The boy ducked down and dodged it – barely.

Most of the volley of bullets missed him, instead splintering the wood of the table as they flew past.

However, one stray bullet thudded into his shoulder. Blood oozed out of the wound as Shinji kicked the table forward as a temporary shield, his instincts honed by piloting the Evangelion kicking in.

Although Shinji certainly wasn't trained as a tactician, he was trained sufficiently in combat to see that the table wouldn't hold for long.

Spinning around to see the van was not too far off, he rolled the table across to it, following the table to protect from the incoming rounds that were still shattering pieces of the table off.

He stood up immediately as he got to that black van, coming around as the table was smashed into by the black-garbed man who was very pissed off that he was still alive.

With a quick burst of speed Shinji quickly ran around to the back of the van, which was still open.

He looked inside and gasped.

On the wall were literally dozens of highly dangerous weapons – guns, plastic explosives, grenades, different assortments of knives and vests of Kevlar.

Without thinking he grabbed at the nearest weapon he could find, spinning around just in time to see the soldier bearing his weapon down at him.

Instinctively Shinji pulled the trigger, the bulky handgun bucking in his hands as he staggered back from the recoil.

The gunman stepped back in shock, blood spurting out of his wounds as the bullets impacted into him.

Shinji continued to fire like a madman, his wounded shoulder screaming at him but he continued to fire until the weapon was depleted.

Only then did the gunman finally crumple to the ground.

Shinji lowered the weapon in shock, realizing what he had just done.

But before he could, everything went black as another gunman hit him in the back of the head with the butt of his rifle.

"This boy is the former pilot of Unit 01," the man stated as he shouldered his weapon. "The client would become…aggravated if he were to be harmed."

"But he's seen what we have done," another said as they came back to the van.

The cleaners' commander nodded. "I'll take him back to the ICA – see what they want to do with him." Turning back to the rest of his comrades, "are the charges in place?"

"Yes sir," the last one said as they got back on the van.

"Good. Activate the remote detonator when we've rounded the next corner back to HQ."

-------

"_Yes, indeed. I'm surprised that a boy like yourself managed to kill a cleaner." _The voice mused.

"What's a…cleaner?" Shinji asked dumbfounded.

_"Cleaners are employed by the ICA if an assassin failed to complete his goal or made a mess out of it. They kill all the witnesses and leave none alive…thankfully rarely used."_

"Then why did they leave me alive?" _I'm better off dead…_

_"Very simply, because the client was an operative of NERV and would be annoyed at seeing you harmed. However… now that you're here you cannot go back."_

"NERV…cannot go back…wait! NO! PLEASE! You can't leave me locked up in here!"

_"My friend, I do not plan to. Because with your killing of a cleaner and skill with the Evangelions, I have found myself another subject."_

Shinji sweated in fear, of what 'subject' meant.

_"The ICA has employed ME to produce assassins for them – genetically engineered, if it can be helped."_

"Oh no…" Shinji mumbled. "Oh no, oh no, oh no…"

_"Do not worry, my friend. I'm sure that after a few…moderations and with a little training you will be fit for their purpose."_

"PLEASE DON'T DO THIS TO ME!" Shinji screamed as several guards came in, carrying the stretcher down the hallway into the operation room. "NO PLEASE! PLEASE! ANYTHING…NOOOOOO!!!"

The door slammed shut.

-------

The old man behind the mike smiled. _My friend, you will be special._

He put his hand on an AMT Hardballer – the exact same one Shinji used to save his own life. _You will be my weapon against the prodigal son – and I will_ _use HIS own assets against him._

He grinned as he turned to the DNA fridge.

Several glass tubes were there, with the label '47' on them.

-------

A/N: Yes, very short chapter, but I just want to get it established. If anyone has not played the Hitman series, namely Hitman 1, either play it or if you want next chapter I can explain it.


	2. 49's training

"Ridiculous." Executive #1 stated.

"Despicable." Executive #4 added.

"Necessary," Executive #2 argued. " This boy saw a messy assassination taking place, saw the cleaners and killed one of them in combat."

"Regardless, the client said no one else who worked for NERV was to be injured!" Executive #3 roared. "If she finds out we have captured him…"

"She shall do no such thing. ICA covers its tracks well, and a woman like her cannot possibly figure out we have taken him."

"Even so, Ikari has been missing for over 24 hours. Either we return him as he is… or take him in for the experiment."

"THAT IS COMPLETELY OUT OF THE QUESTION! The doctor may be a genius, but we do not know what he is capable of! Only a minor percentage of the runaways and orphans are undergoing genetic alterations and already the majority of them have become patients for a mental hospital!"

Executive #2 become silent. "It has already been done."

All the executives of ICA fell quiet.

Executive #2 spoke again. "His hair has already been shaved for him to undergo surgery. We will use it to create a clone of him."

"But it may take years before the clone grows to his age!"

"Not if we use a specialized process, though his neural pathways will become severely damaged. This will not be a factor in this case. I will organize a train bombing and plant the clone's body onto it," Executive #3 replied.

"Then it is decided," Executive #1 concluded. "If none of you gentlemen have anything left to say, I have other matters to attend to."

One by one, the four computer screens around the table switched off and the meeting room became silent once more.

-------

**5 years later**

A lone figure approached the door to the Smith Mansion.

Several guards came up to him. "Halt! State your business here!" the lead one barked snappily.

"Package for Mr. Smith," the young postman said, holding out the medium-sized box.

The man nodded. "Very well – go in and leave it in the foyer. I will inform the butler to pick it up."

Just as the postman was about to go in, the guard stopped him, holding out a portable metal detector.

He scanned him quickly from head to toe, but just as he was scanning the box the detector let out a loud beep.

"What is in this?" the guard demanded, about to take his gun out.

The postman shrugged. "They don't tell it to us deliverymen. Why don't you ask Mr. Smith?"

The guard appeared to consider this for a moment. "Very well, you may go in."

The postman nodded as he entered the large foyer.

A butler quickly came in. "Thank you very much, I'll take it from here."

The postman smiled politely as he gave him the package, his hands slipping behind his back.

Immediately as the butler turned, 49 tightened his grip on the fibre wire as he flung it around the man's neck, pulling it back swiftly in a single move. The older man gagged, but otherwise did not make a sound as he closed his eyes and lent back.

49 looked around wildly before dragging the man to a closet. There he quickly changed into the other man's outfit before picking up the package, walking up the staircase as he slid his gloved hand into a hidden compartment.

He knocked on the main door before opening it.

There he was greeted with a Mr. Smith snoozing in the bed.

"Yes?" the man asked groggily.

"You have a package sir," 49 said in a near-perfect imitation of the dead butler's voice.

"Bring it over here…" Mr. Smith yawned as he struggled up, his fat bulk being a severe limit.

49 walked over to the side of the bed and bent down, tightening his grip on the hidden pistol inside.

"So what is it?" the millionaire asked as he looked down on it.

The assassin grinned sadistically as he spoke in his normal tone. "Your death!" he pulled the trigger on the silenced pistol concealed inside.

The bullet burst through the cardboard easily, entering Mr. Smith's head as the man slumped down.

49 showed no emotion as he stood up, taking the concealed AMT Hardballer out of the package and pocketing it as he ran to the room window.

Opening it, the genetically enhanced assassin leapt out in one effortless motion, landing on the grounds as he ran away, scaling the fence that was his only obstacle easily and escaping to freedom.

-------

Immediately as he jumped the fence, the simulation melted away into its normal green grid against black look.

_"Well done my friend – and record time too! Few have gotten to this room and passed."_

49 nodded in acknowledgement as he walked into the elevator.

_"Go to the gym my friend and work there until the guards come for you then rest. You have most certainly earned it."_

-------

Doctor Ort-Meyers leant back in his chair and smiled. Everything was going as he had planned…

It had been many years since that traitorous 47 had killed him and his soul transferred into another clone of himself. Since then, although his research had been set back slightly it had progressed farther than he had possibly imagined.

No other agencies could replicate his success, because they did not have one thing: 47's DNA. Other agencies could create clones, yes, but they were merely empty vessels. No true life was inside them, and even for the stark, remote possibility that the procedure did work, they usually turned out insane when growing.

Not like 47 – he was a perfect, working clone. His DNA was valued by any agency for it to fill in the gaps in their cloning programs.

Although Dr. Ort-Meyer didn't clone him anymore (the fact that he DID break his neck would be a significant factor) he had found another incredible revelation.

Because 47's DNA was a mix of different people that ultimately resulted in a completely unique DNA of his own, he found that by copying key genes out of 47's DNA and inserting them into others he had for himself a person with all of 47's intelligence, strength, speed and stamina.

However but of course there were side effects – insanity and delirium originally but that was because of the conflicting personalities resulting from this.

But by getting someone who was either depressed, willing to accept the new personality or brainwashing them to automatically accept it this would work.

Even with this, Ort-Meyer didn't want someone with just 47's capabilities. He wanted someone BETTER.

And so it had come to this – this young person known formerly as Shinji Ikari. His mind had been wiped, genetics replaced not only with 47's but also with a huge variety from all over the world – assassins, soldiers, criminals, masterminds, not always willingly either.

At the end, to prevent Shinji from either going insane, his neural pathways failing or his appearance becoming a mess because of the confused genetics the 'base' DNA of Shinji remained to maintain his normal appearance and grow like he would, albeit slightly altered because of the different genetics.

But it had all been worth it – Ort-Meyers now had a perfect soldier, warrior, and assassin in every respect and he would be praised and feared by not only the ICA, but also the underworld.

He was Agent 49.


End file.
